WGCNA: allowWGCNAThreads – R documentation

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allowWGCNAThreads

Allow and disable multi-threading for certain WGCNA calculations

Description

These functions allow and disable multi-threading for WGCNA calculations that can optionally be multi-threaded, which includes all functions using cor or bicor functions.

Usage

allowWGCNAThreads(nThreads = NULL)

enableWGCNAThreads(nThreads = NULL)

disableWGCNAThreads()

WGCNAnThreads()

Arguments

nThreads

Number of threads to allow. If not given, the number of processors online (as reported by system configuration) will be used. There appear to be some cases where the automatically-determined number is wrong; please check the output to see that the number of threads makes sense. Except for testing and/or torturing your system, the number of threads should be no more than the number of actual processors/cores.

Details

allowWGCNAThreads enables parallel calculation within the compiled code in WGCNA, principally for calculation of correlations in the presence of missing data. This function is now deprecated; use enableWGCNAThreads instead.

enableWGCNAThreads enables parallel calculations within user-level R functions as well as within the compiled code, and registers an appropriate parallel calculation back-end for the operating system/platform.

disableWGCNAThreads disables parallel processing.

WGCNAnThreads returns the number of threads (parallel processes) that WGCNA is currently configured to run with.

Value

allowWGCNAThreads, enableWGCNAThreads, and disableWGCNAThreads return the maximum number of threads WGCNA calculations will be allowed to use.

Note

Multi-threading within compiled code is not available on Windows; R code parallelization works on all platforms.

Author(s)

Peter Langfelder

WGCNA

Weighted Correlation Network Analysis

v1.70-3

GPL (>= 2)

Authors

Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang

Initial release

2021-02-17